JAL-2629 fix HMMER validation fail due to checking for HMM incorrectly

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 7af3abc..7c0ac95 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -112,6 +112,10 @@ public class Preferences extends GPreferences
   
   public static final String HMMER_PATH = "HMMER_PATH";
 
+  public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
+
+  public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
+
   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 
   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
@@ -1312,7 +1316,7 @@ public class Preferences extends GPreferences
   {
     HMMBuildThread hmmbuild = new HMMBuildThread(alignment);
     hmmbuild.hmmbuildWaitTillComplete();
-    SequenceI hmmSeq = alignment.getSequenceAt(1);
+    SequenceI hmmSeq = alignment.getSequenceAt(0);
     HiddenMarkovModel hmm;
     if (hmmSeq.isHMMConsensusSequence() && hmmSeq.getHMM() != null)
     {